Genome-wide association study identified five quantitative trait loci and two candidate genes for digestive traits in Suhuai pigs
Anim Genet. 2024 Apr 15. doi: 10.1111/age.13430. Online ahead of print.ABSTRACTThis work aimed to identify markers and candidate genes underlying porcine digestive traits. In total, 331 pigs were genotyped by 80 K Chip data or 50 K Chip data. For apparent neutral detergent fiber digestibility, a total of 19 and 21 candidate single nucleotide polymorphisms (SNP) were respectively identified using a genome-wide efficient mixed-model association algorithm and linkage-disequilibrium adjusted kinship. Among them, three quantitative trait locus (QTL) regions were identified. For apparent acid detergent fiber digestibility, a tot...
Source: Animal Genetics - April 15, 2024 Category: Genetics & Stem Cells Authors: Kaijun Li Liming Hou Taoran Du Guang Pu Chenxi Liu Gensheng Liu Juan Zhou Ruihua Huang Qingbo Zhao Pinghua Li Source Type: research
Multiplex fluorescent amplification-refractory mutation system PCR method for the detection of 10 genetic defects in Holstein cattle and its comparison with the KASP genotyping assay
This study was conducted to develop a single-tube multiplex fluorescent amplification-refractory mutation system (mf-ARMS) PCR method for efficient genotyping of these 10 genetic defects and to compare its efficiency with the kompetitive allele specific PCR (KASP) genotyping assay. The mf-ARMS PCR method introduced 10 sets of tri-primers optimized with additional mismatches in the 3' end of wild and mutant-specific primers, size differentiation between wild and mutant-specific primers, fluorescent labeling of universal primers, adjustment of annealing temperatures and optimization of primer concentrations. The genotyping o...
Source: Animal Genetics - April 15, 2024 Category: Genetics & Stem Cells Authors: Md Yousuf Ali Khan Dongmei Dai Xin Su Jia Tian Jiamin Zhou Liqin Ma Yachun Wang Wan Wen Yi Zhang Source Type: research
Genome-wide association study identifies a novel candidate gene for egg production traits in chickens
Anim Genet. 2024 Apr 11. doi: 10.1111/age.13427. Online ahead of print.ABSTRACTQingyuan partridge chicken is a renowned indigenous yellow broiler breed in China. Egg production traits are important economic traits for chickens. With the decreasing cost of whole genome resequencing, identifying candidate genes with more precision has become possible. In order to identify molecular markers and candidate genes associated with egg production traits, we conducted genome-wide association studies based on the resequencing data of 287 female Qingyuan partridge chickens. For each hen, age at first egg and egg laying rate were recor...
Source: Animal Genetics - April 12, 2024 Category: Genetics & Stem Cells Authors: Huimin Kang Yuedan Lu Weitu Zhang Guohong Hua Jiankang Gan Xuqing Deng Zhengfen Zhang Hua Li Source Type: research
Genome-wide association study identifies a novel candidate gene for egg production traits in chickens
Anim Genet. 2024 Apr 11. doi: 10.1111/age.13427. Online ahead of print.ABSTRACTQingyuan partridge chicken is a renowned indigenous yellow broiler breed in China. Egg production traits are important economic traits for chickens. With the decreasing cost of whole genome resequencing, identifying candidate genes with more precision has become possible. In order to identify molecular markers and candidate genes associated with egg production traits, we conducted genome-wide association studies based on the resequencing data of 287 female Qingyuan partridge chickens. For each hen, age at first egg and egg laying rate were recor...
Source: Animal Genetics - April 12, 2024 Category: Genetics & Stem Cells Authors: Huimin Kang Yuedan Lu Weitu Zhang Guohong Hua Jiankang Gan Xuqing Deng Zhengfen Zhang Hua Li Source Type: research
Genome-wide association study identifies a novel candidate gene for egg production traits in chickens
Anim Genet. 2024 Apr 11. doi: 10.1111/age.13427. Online ahead of print.ABSTRACTQingyuan partridge chicken is a renowned indigenous yellow broiler breed in China. Egg production traits are important economic traits for chickens. With the decreasing cost of whole genome resequencing, identifying candidate genes with more precision has become possible. In order to identify molecular markers and candidate genes associated with egg production traits, we conducted genome-wide association studies based on the resequencing data of 287 female Qingyuan partridge chickens. For each hen, age at first egg and egg laying rate were recor...
Source: Animal Genetics - April 12, 2024 Category: Genetics & Stem Cells Authors: Huimin Kang Yuedan Lu Weitu Zhang Guohong Hua Jiankang Gan Xuqing Deng Zhengfen Zhang Hua Li Source Type: research
The landscape of allelic expression and DNA methylation at the bovine SGCE/PEG10 locus
In this study, we investigated allele expression of 14 genes of the SGCE/PEG10 locus in bovine somatic tissues and term placenta using a single nucleotide polymorphism (SNP)-based sequencing method. In addition to SGCE and PEG10, two conserved paternally expressed genes in human and mice, five other genes (TFPI2, GNG11, ASB4, PON1, and PON3) were paternally expressed. Three genes, BET1, COL1A2, and CASD1, exhibited tissue-specific monoallelic expression. CALCR showed monoallelic expression in tissues but biallelic expression in the placenta. Three genes, GNGT1, PPP1R9A, and PON2, showed biallelic expression in cattle. Five...
Source: Animal Genetics - April 10, 2024 Category: Genetics & Stem Cells Authors: Yinjiao Zhang Cui Zhang Weina Chen Haonan Huo Shujing Li Wenli Yu Lanjie Jin Kun Wang Shijie Li Source Type: research
Identification of candidate genes associated with milk production and mastitis based on transcriptome-wide association study
Anim Genet. 2024 Apr 9. doi: 10.1111/age.13422. Online ahead of print.ABSTRACTGenetic research for the assessment of mastitis and milk production traits simultaneously has a long history. The main issue that arises in this context is the known existence of a positive correlation between the risk of mastitis and lactation performance due to selection. The transcriptome-wide association study (TWAS) approach endeavors to combine the expression quantitative trait loci and genome-wide association study summary statistics to decode complex traits or diseases. Accordingly, we used the farmgtex project results as a complete bovin...
Source: Animal Genetics - April 10, 2024 Category: Genetics & Stem Cells Authors: Sevda Hosseinzadeh Seyed Abbas Rafat Arash Javanmard Lingzhao Fang Source Type: research
The landscape of allelic expression and DNA methylation at the bovine SGCE/PEG10 locus
In this study, we investigated allele expression of 14 genes of the SGCE/PEG10 locus in bovine somatic tissues and term placenta using a single nucleotide polymorphism (SNP)-based sequencing method. In addition to SGCE and PEG10, two conserved paternally expressed genes in human and mice, five other genes (TFPI2, GNG11, ASB4, PON1, and PON3) were paternally expressed. Three genes, BET1, COL1A2, and CASD1, exhibited tissue-specific monoallelic expression. CALCR showed monoallelic expression in tissues but biallelic expression in the placenta. Three genes, GNGT1, PPP1R9A, and PON2, showed biallelic expression in cattle. Five...
Source: Animal Genetics - April 10, 2024 Category: Genetics & Stem Cells Authors: Yinjiao Zhang Cui Zhang Weina Chen Haonan Huo Shujing Li Wenli Yu Lanjie Jin Kun Wang Shijie Li Source Type: research
Identification of candidate genes associated with milk production and mastitis based on transcriptome-wide association study
Anim Genet. 2024 Apr 9. doi: 10.1111/age.13422. Online ahead of print.ABSTRACTGenetic research for the assessment of mastitis and milk production traits simultaneously has a long history. The main issue that arises in this context is the known existence of a positive correlation between the risk of mastitis and lactation performance due to selection. The transcriptome-wide association study (TWAS) approach endeavors to combine the expression quantitative trait loci and genome-wide association study summary statistics to decode complex traits or diseases. Accordingly, we used the farmgtex project results as a complete bovin...
Source: Animal Genetics - April 10, 2024 Category: Genetics & Stem Cells Authors: Sevda Hosseinzadeh Seyed Abbas Rafat Arash Javanmard Lingzhao Fang Source Type: research
Study on the origin of the Baise horse based on whole-genome resequencing
In this study, whole-genome resequencing data from 236 horses of seven Chinese indigenous horse breeds, five foreign horse breeds, and four Przewalski's horses were used to investigate the relationships between the Baise horse and other horse breeds. The results showed that foreign horse breeds had no significant impact on the formation of the Baise horse. The two southwestern horse populations, the Debao pony and the Jinjiang horse, exhibit the closest genetic affinity with the Baise horse. This is consistent with their adjacent geographical distribution. Analysis of the migration route revealed a gene flow from the Chako...
Source: Animal Genetics - April 7, 2024 Category: Genetics & Stem Cells Authors: Xiaoran Lin Mo Feng Ying Li Yu Liu Min Wang Yuanyuan Li Tao Yang Chunjiang Zhao Source Type: research
A novel QTL region for pH and meat color in Duroc pigs
Anim Genet. 2024 Apr 7. doi: 10.1111/age.13426. Online ahead of print.ABSTRACTOne of the most important processes that occur during the transformation of muscle to meat is the pH decline as a consequence of the post-mortem metabolism of muscle tissue. Abnormal pH declines lead to pork defects such as pale, soft, and exudative meat. There is genetic variance for ultimate pH and the role of some genes on this phenotype is well established. After conducting a genome-wide association study on ultimate pH using 526 purebred Duroc pigs, we identified associated regions on Sus scrofa chromosomes (SSC) 3, 8, and 15. Functional can...
Source: Animal Genetics - April 7, 2024 Category: Genetics & Stem Cells Authors: Eduard Molinero Ramona N Pena Joan Estany Roger Ros-Freixedes Source Type: research
Study on the origin of the Baise horse based on whole-genome resequencing
In this study, whole-genome resequencing data from 236 horses of seven Chinese indigenous horse breeds, five foreign horse breeds, and four Przewalski's horses were used to investigate the relationships between the Baise horse and other horse breeds. The results showed that foreign horse breeds had no significant impact on the formation of the Baise horse. The two southwestern horse populations, the Debao pony and the Jinjiang horse, exhibit the closest genetic affinity with the Baise horse. This is consistent with their adjacent geographical distribution. Analysis of the migration route revealed a gene flow from the Chako...
Source: Animal Genetics - April 7, 2024 Category: Genetics & Stem Cells Authors: Xiaoran Lin Mo Feng Ying Li Yu Liu Min Wang Yuanyuan Li Tao Yang Chunjiang Zhao Source Type: research
A novel QTL region for pH and meat color in Duroc pigs
Anim Genet. 2024 Apr 7. doi: 10.1111/age.13426. Online ahead of print.ABSTRACTOne of the most important processes that occur during the transformation of muscle to meat is the pH decline as a consequence of the post-mortem metabolism of muscle tissue. Abnormal pH declines lead to pork defects such as pale, soft, and exudative meat. There is genetic variance for ultimate pH and the role of some genes on this phenotype is well established. After conducting a genome-wide association study on ultimate pH using 526 purebred Duroc pigs, we identified associated regions on Sus scrofa chromosomes (SSC) 3, 8, and 15. Functional can...
Source: Animal Genetics - April 7, 2024 Category: Genetics & Stem Cells Authors: Eduard Molinero Ramona N Pena Joan Estany Roger Ros-Freixedes Source Type: research
Study on the origin of the Baise horse based on whole-genome resequencing
In this study, whole-genome resequencing data from 236 horses of seven Chinese indigenous horse breeds, five foreign horse breeds, and four Przewalski's horses were used to investigate the relationships between the Baise horse and other horse breeds. The results showed that foreign horse breeds had no significant impact on the formation of the Baise horse. The two southwestern horse populations, the Debao pony and the Jinjiang horse, exhibit the closest genetic affinity with the Baise horse. This is consistent with their adjacent geographical distribution. Analysis of the migration route revealed a gene flow from the Chako...
Source: Animal Genetics - April 7, 2024 Category: Genetics & Stem Cells Authors: Xiaoran Lin Mo Feng Ying Li Yu Liu Min Wang Yuanyuan Li Tao Yang Chunjiang Zhao Source Type: research
A novel QTL region for pH and meat color in Duroc pigs
Anim Genet. 2024 Apr 7. doi: 10.1111/age.13426. Online ahead of print.ABSTRACTOne of the most important processes that occur during the transformation of muscle to meat is the pH decline as a consequence of the post-mortem metabolism of muscle tissue. Abnormal pH declines lead to pork defects such as pale, soft, and exudative meat. There is genetic variance for ultimate pH and the role of some genes on this phenotype is well established. After conducting a genome-wide association study on ultimate pH using 526 purebred Duroc pigs, we identified associated regions on Sus scrofa chromosomes (SSC) 3, 8, and 15. Functional can...
Source: Animal Genetics - April 7, 2024 Category: Genetics & Stem Cells Authors: Eduard Molinero Ramona N Pena Joan Estany Roger Ros-Freixedes Source Type: research
